I don't think there is too much of a problem with the WCC, problem probably lie in the candidate for the challenger. A good example would be in the Anand - Gelfard.
The problem with the WCC currently is that deciding the champion based on who wins a rapid game or a blitz armageddon game is ludicrous. It has very little to do with determining who is the best match player at standard time controls, which is what it's supposed to be all about.
The other problem is that in cases where the stronger rapid/blitz player is weaker at standard time controls, the rational strategy for them is to try to force a draw through any means necessary in every game and save the fight for the rapid/blitz play -- the Grischuk strategy, which is contrary to the spirit of the WC.
Another problem is that when you have two players (like Gelfand and Anand) who are no longer at the very top of the world, the next match will only have 1 new player in it, as we saw here. It would have been better if after neither Anand nor Gelfand proved really deserving of the title in 2012, the top two finishers in the 2013 qualifers would have played for the title, and we could have had a Carlsen-Kramnik match, and all the discussion about whether Carlsen beating Anand really means anything since Kramnik is who he really needs to beat would be redundant. Instead, we'll have to wait until perhaps 2014.
I don't think there is too much of a problem with the WCC, problem probably lie in the candidate for the challenger. A good example would be in the Anand - Gelfard.